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Table 3 Similarity of CNVs detected between programs using HapMap data

From: Comparative analysis of copy number variation detection methods and database construction

Programs PennCNV Birdseye (part of Birdsuite) Birdsuite DNAcopy CGHseg
PennCNV
[12417/6895]
- 55.1/62.2*
(56.4/61.9)
62.5/75.2
(63.1/76.7)
49.2/63.5 (51.5/65.3)
   23.2/26.8
(23.8/26.9)
  
Birdseye (part of Birdsuite)
[14794/10102]
62.2/69.8
(82.8/88.5)
- 57.5/68.4
(69.8/82.6)
40.7/52.4
(49.1/61.6)
Birdsuite
[56476/44150]
68.0/74.3
(90.3/93.3)
  68.8/73.9
(84.5/89.4)
47.0/54.4
(57.5/63.3)
DNAcopy
[6748/4849]
37.7/40.8
(50.7/53.8)
29.6/31.8
(38.0/40.4)
- 61.1/68.6
(62.1/68.6)
   13.8/15.0
(16.4/17.7)
  
CGHseg
[3648/2401]
13.8/17.4
(17.1/20.9)
10.1/12.3
(11.6/13.9)
32.1/35.6
(27.4/32.0)
-
   4.2/5.2
(4.6/5.6)
  
  1. Similarity: percentage of CNVs detected using the program in row, which is also detected using the program in column. That is, each program in row is regard as golden standard.
  2. *Sensitivity with 80%overlap/5%overlap of CNV segments
  3. (): represents deletion-only data
  4. []: represents total number of CNVs/total number of CNV deletions.